Zinc in PDB 6wkq: 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin

The structure of 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin, PDB code: 6wkq was solved by G.Minasov, L.Shuvalova, M.Rosas-Lemus, O.Kiryukhina, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.92 / 1.98
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	166.247, 166.247, 98.139, 90.00, 90.00, 120.00
R / Rfree (%)	16.2 / 18

The structure of 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Zinc atom in the 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin (pdb code 6wkq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin, PDB code: 6wkq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4401 b:39.6 occ:1.00 NE2 B:HIS4336 2.1 51.3 1.0 SG B:CYS4327 2.3 41.2 1.0 SG B:CYS4343 2.3 42.2 1.0 SG B:CYS4330 2.3 40.5 1.0 CD2 B:HIS4336 3.0 51.1 1.0 CE1 B:HIS4336 3.1 52.4 1.0 CB B:CYS4327 3.2 40.4 1.0 CB B:CYS4343 3.3 47.0 1.0 CB B:CYS4330 3.4 40.0 1.0 N B:CYS4330 3.6 41.5 1.0 CA B:CYS4330 3.9 40.3 1.0 CG B:HIS4336 4.2 53.7 1.0 ND1 B:HIS4336 4.2 53.9 1.0 CA B:CYS4343 4.5 50.3 1.0 CB B:TYR4329 4.5 45.7 1.0 C B:TYR4329 4.6 43.0 1.0 CA B:CYS4327 4.6 38.7 1.0 CB B:LYS4346 4.8 39.3 1.0 CA B:TYR4329 4.9 44.5 1.0 O B:CYS4327 5.0 37.5 1.0 N B:LYS4346 5.0 35.8 1.0 C B:CYS4327 5.0 39.2 1.0

Zinc binding site 2 out of 4 in the 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4402 b:49.4 occ:1.00 SG B:CYS4381 2.3 47.3 1.0 SG B:CYS4370 2.3 52.5 1.0 SG B:CYS4373 2.3 51.7 1.0 SG B:CYS4383 2.3 59.8 1.0 CB B:CYS4370 3.2 52.2 1.0 CB B:CYS4373 3.3 53.4 1.0 CB B:CYS4383 3.4 64.6 1.0 CB B:CYS4381 3.5 50.5 1.0 N B:CYS4373 3.6 53.9 1.0 CA B:CYS4373 4.0 52.7 1.0 O B:HOH4523 4.0 47.3 1.0 CA B:CYS4381 4.0 50.1 1.0 N B:CYS4383 4.1 63.2 1.0 CA B:CYS4383 4.3 65.3 1.0 CB B:VAL4372 4.4 59.0 1.0 N B:SER4382 4.5 56.1 1.0 C B:CYS4381 4.6 51.7 1.0 CA B:CYS4370 4.6 51.0 1.0 C B:VAL4372 4.6 56.1 1.0 C B:CYS4373 4.9 50.5 1.0 CG1 B:VAL4372 4.9 59.8 1.0 CA B:VAL4372 4.9 57.8 1.0 N B:GLY4374 4.9 48.3 1.0 N B:VAL4372 5.0 56.7 1.0

Zinc binding site 3 out of 4 in the 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn4401 b:36.7 occ:1.00 NE2 D:HIS4336 2.1 43.6 1.0 SG D:CYS4327 2.3 39.0 1.0 SG D:CYS4343 2.3 39.0 1.0 SG D:CYS4330 2.3 38.9 1.0 CD2 D:HIS4336 3.1 45.2 1.0 CE1 D:HIS4336 3.1 45.1 1.0 CB D:CYS4327 3.2 37.7 1.0 CB D:CYS4343 3.3 43.4 1.0 CB D:CYS4330 3.4 37.1 1.0 N D:CYS4330 3.5 38.1 1.0 CA D:CYS4330 3.9 36.9 1.0 ND1 D:HIS4336 4.2 47.3 1.0 CG D:HIS4336 4.2 49.2 1.0 O D:HOH4549 4.3 33.0 0.5 CA D:CYS4343 4.4 45.7 1.0 C D:TYR4329 4.5 39.0 1.0 CB D:TYR4329 4.5 43.1 1.0 CA D:CYS4327 4.6 36.6 1.0 CB D:LYS4346 4.9 40.5 1.0 CA D:TYR4329 4.9 40.5 1.0 N D:LYS4346 5.0 34.9 1.0 C D:CYS4327 5.0 36.4 1.0

Zinc binding site 4 out of 4 in the 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn4402 b:54.3 occ:1.00 SG D:CYS4381 2.3 54.8 1.0 SG D:CYS4370 2.3 58.8 1.0 SG D:CYS4373 2.3 58.4 1.0 SG D:CYS4383 2.3 71.7 1.0 CB D:CYS4370 3.2 57.4 1.0 CB D:CYS4373 3.4 58.1 1.0 CB D:CYS4383 3.4 79.8 1.0 CB D:CYS4381 3.5 57.8 1.0 N D:CYS4373 3.6 59.0 1.0 CA D:CYS4381 4.0 57.0 1.0 CA D:CYS4373 4.1 56.6 1.0 N D:CYS4383 4.2 78.7 1.0 CA D:CYS4383 4.4 82.9 1.0 CB D:VAL4372 4.5 64.9 1.0 N D:SER4382 4.5 65.9 1.0 C D:CYS4381 4.6 60.6 1.0 CA D:CYS4370 4.6 55.9 1.0 C D:VAL4372 4.7 61.5 1.0 C D:CYS4373 4.9 51.5 1.0 CA D:VAL4372 4.9 63.3 1.0 N D:GLY4374 5.0 49.9 1.0 N D:VAL4372 5.0 62.4 1.0 CG1 D:VAL4372 5.0 65.2 1.0

G.Minasov, L.Shuvalova, M.Rosas-Lemus, O.Kiryukhina, K.J.F.Satchell. 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin. To Be Published.